Naruto's Secret
by Aiden Ravelle
Summary: Naruto goes missing and his team goes out to search for him.


First Naruto fic, don't own anything, sorry for anything to OOC. They know a bit more/had more training than the beginning and Tsunade is hokage but sasuke hasn't been taken to orochimaru. Also, I started this months ago and have written in bits and bits, and I've tried to make it all work, but I'm sorry if any of the parts didn't mesh together right. I've legit been writing this for like at least 6 months...

Thanks for reading.

Naruto awoke with a start, hearing a loud noise in his room. Next thing he sees is a black bag over his head and a bump on his head making everything fuzzy and draining him of the power to scream. He tried to fight, but a few wounds later and he was fully unconscious.

"Kakashi-sensei, you are always late!" Sakura complained loudly.

"Naruto is never late though," Sasuke pointed out wishing to train with his rival.

"Hmm," Kakashi sighed, "I'll go check on him."

"Let's go find him," Sasuke told Sakura.

"We could just stay here and train together while Kakashi-sensei looks for him," Sakura suggested, but Sasuke shook his head and walked away.

The group came up to Naruto's apartment, the younger two never seeing it before.

"I didn't know he had such a small place," Sakura analyzed.

"Strange," Kakashi said noticing the open door.

Glancing inside the group found the apartment a mess. Broken glass, blood stains on the bed, and furniture smashed on the floor.

"I know Naruto is a messy person, but this can't be good, can it?" Sakura asked starting to get worried.

Sasuke noticed how wide Kakashi's eye got before he calmly looked at them and said, "I need to go talk to someone, you guys go get some lunch," he waved his hand and disappeared.

"Sasuke, where do you think Naruto is?"

"I don't know," he said quietly, thinking of Kakashi's reaction.

Naruto awoke chained up to a wall, blinking the pain away.

"Where am I?" he questioned loudly to whoever would answer. He looked around and noticed he was in a stone cell with a barred door.

"Ah you are awake I see," said a strange looking man who approached the door. His hair was wild and looked like it hadn't been washed in decades, "Not to worry, we just need to take out the nine tails, should only be a few more days until we have the equipment needed."

"Who are you?" Naruto asked angrily.

"Who I am does not matter, just a scientist, but who you are, is important, isn't it?"

Naruto was confused at the comment but shook off his confusion, "Why do you need the nine tails?"

"He is a great source of power, which we will use to destroy the very village you try to protect," the man laughed wildly.

"What do you have against the leaf village?" Naruto questioned fighting against his shackles.

"Wouldn't you like to know," the man walked off laughing.

"That's why I asked," Naruto mumbled. He tried to use his chakra to make clones. When that didn't work he tried all of the other jutsus he could think of but nothing worked. Frustrated, he decided to wait for the scientist to come back.

After what seemed like hours, the scientist came back, "Don't you just love my chakra canceling shackles?"

Naruto jerked up surprised. The man opened the door.

"I'd like to test some of my inventions on you if you don't mind," the scientist chuckled, "It's not like you can stop me if you do mind though."

Naruto had become silent and unanswering, hoping the man would accidentally give Naruto a means of escape.

"My goal is to get the ninetails to power my ultimate weapon, similar to a bomb. But, I have many other inventions which need testing and it really is hard to find test subjects who are willing," he smiled coldly, "Let's start with this one."

The scientist attached a collar around Naruto's neck as Naruto flailed to keep him away.

Once the collar was on the scientist said, "The fox is very similar to a dog, sometimes you need a bit of discipline," he pressed a button on a small remote which sent shock waves through Naruto's body. All of the muscles tensed up in his body causing him to scream out in pain.

"Looks like that one works, but I think I'll leave it on you in case you need some more discipline."

He pulled out another device which he attached to a bar on the door, "This is meant to be placed anywhere to help keep out intruders," The man left the room and closed the door, "Don't want to get in the way now."

He pressed a button on the machine, which at first did nothing, but as soon as Naruto shifted, it shot a shuriken at him which hit his arm. He flinched at the pain, and it shot another one.

"If you keep flinching, it will keep shooting. It's motion detected," the man laughed cruelly as he walked away, "More inventions to test later though, have fun."

"This is bad," Tsunade spoke aloud putting her hands on her desk.

"Shizune, call the anbu. I want to know how someone got in or out of this village," Tsunade demanded as Shizune nodded.

"Of course, he may still be in the village, but there was clearly blood and some sort of struggle," Kakashi told the Hokage.

"They must be after the ninetails, but who knows if it's to kill him or to get the ninetail power," Tsunade said the obvious. Naruto had run-ins with trouble all of his life, mostly from villagers who hated the nine tails and along with that, hated him.

An anbu member quickly arrived, "No one came into or left the village in the last 24 hours. Nothing has looked suspicious."

"I want all anbu on the lookout for Naruto Uzumaki," the Hokage told the anbu who bowed and left.

"Kakashi, I want your team to be on the lookout was well," Tsunade told him.

"Uh," Kakashi started, "they don't know he has the ninetail spirit in him. Should I tell them or should we just look for him, or…?" Kakashi trailed off.

"Damn," Tsunade thought for a minute, "As teammates, they should know all there is to know about each other, especially something like this that can cause danger to any one of them. As their leader, you are in charge of telling them."

Kakashi nodded and left.

He dropped down in front of Ichiraku Ramen, which was Naruto's favorite place. He walked in and noticed Sakura, Sasuke, and Iruka talking and eating.

"We thought we might find Naruto here," Sakura informed.

"They told me Naruto didn't show up today," Iruka questioned, "Did you find him?"

Kakashi shook his head.

"You don't think…" Iruka suggested.

Kakashi gave a nod, "Team, we have a mission."

"I want to help," Iruka informed.

"You have classes to get to," Kakashi reminded him.

"This could be dangerous," Iruka burst, "You have no idea what could happen!"

"Iruka," Kakashi said, "The anbu is already involved, let us do our work."

"Sensei, what is going on?" Sakura said cutting Iruka off from arguing more.

"Our mission is to find Naruto. This could be dangerous and we don't know who could have taken him," Kakashi informed.

"Why would anyone want that idiot?" Sasuke wondered coolly.

"Yeah, what would anyone need him for?" Sakura asked.

"You know nothing about him do you?" Iruka asked irritated.

"Iruka, this is my team, and my mission, I will tell them what they need to know when they need to know it, understood?" Kakashi sighed.

Iruka gave up his frustration and replaced it with a worried look as he headed off to do his duties.

"All you need to know _right now_ is Naruto is most likely in danger, and we need to find him fast," Kakashi informed as Sakura and Sasuke nodded.

Naruto tried to get the shuriken to cut through the shackles but it kept hitting his arms or face. He sighed, and looked at a small cut on his hand.

'Generally I heal by now, right?' Naruto wondered.

'It's suppressing my chakra too,' Kurama informed.

'That makes sense,' Naruto thought to the fox spirit.

'We are in danger. I can't even help you out with the shackles on,' the ninetails told the boy.

"Looks like you had fun with that one," the scientist came up to the bars and took down the shuriken shooter.

"Hmph," Naruto mumbled glad he could at least shift his muscles again.

"Before I continue with more devices, I promised the ones who captured you they could have a go at you," the scientist cackled.

Two large men came to the bars, both with masks on so Naruto could not tell who they were. They moved more like thugs than shinobi.

Naruto could only stand there as they came at him. Kicking, punching, whatever they could do. He tried to stay quiet and not give them the pleasure of him being in pain. He'd been beaten up before for being the ninetails jinchuriki but never this bad. When he started coughing up blood, the scientist spoke up, "He still needs to live for a little while; you've had your fun."

Naruto slumped against the wall, unable to sit the way he was chained up. He kept coughing for a few more minutes until he threw up, having not eaten all day it was mostly just blood that came out.

"I guess I'll let you rest for now, but we will get to more testing later," the scientist left him in silence.

"It will help us find him if we know why he was taken," Sasuke mentioned after a while.

"Well it's not like they left any clues, I don't see why they'd want him anyway," Sakura replied.

"Enough," Kakashi said with a slight anger in his voice, "There are some things you should know about Naruto. I just didn't want to be the one to tell you."

He leaned against a tree and motioned for the group to sit down while he told his story. "You've heard of the Ninetails that wreaked havoc on the village. There are actually 9 different tailed beasts that exist. One of them was Shukaku, the one tailed beast, which resides in Gaara."

"Oh yeah," Sakura remembered Gaara going a bit crazy.

"Well, all of the tailed beasts reside in people, who are called jinchuriki. Now you have to understand, these people generally have the beasts put into them when they are young, and have no choice over it." Kakashi paused before spitting out, "Naruto is a jinchuriki."

Sasuke and Sakura gasped.

"So they want the tailed beast in him," Sasuke concluded.

"The tailed beast gives him some power, such as it helps heal him a bit faster than normal people would heal. However, the beast also brings danger, like how the tailed beasts want to be freed from the jinchuriki, overtaking their bodies, like you saw with Gaara. Many jinchuriki are looked down on because the beasts do harm many people, and once someone knows the beast is in them they only see the beast, not the person the beast is in. That is why no one your age knows he has a beast inside of him, to give him a fair chance to make friends. However, the older members of the village know and I'm not sure if you've noticed, but many people hate him."

"I thought it was just because he was a dumbass," Sasuke admitted.

"It sounds dangerous," Sakura admitted, "I've never noticed that the villagers don't like him."

"He's had some run-ins, but the anbu and the hokage keep a close eye on him," Kakashi told them.

"So what happened now?" Sasuke wondered.

"No one knows, but we can assume he's in danger and whoever has him wants the ninetails power," Kakashi replied.

"He's the _ninetails jinchurik_ i?" Sakura looked surprised.

"No wonder the villagers hate him," Sasuke said in understanding.

"We need to find him soon," Kakashi fully stood back up.

Naruto was unsure if he kept falling asleep or if he was passing out but he kept waking with pain in his wrists from hanging there.

'I can't figure a way out if they don't unhook me,' Naruto thought.

'I can try to take over,' Kurama suggested. Naruto had let Kurama take over a few times before, but knew not to fully trust the fox. But with both of their lives at stake he knew he'd have to risk it.

'With the chakra blocking shackles will it work?' Naruto asked.

Naruto felt his body heating up and power flowing through him, but he still couldn't break free of the shackles.

'No luck,' Naruto sighed.

'Your teammates might come for you,' Kurama suggested.

The usually cheerful Naruto was starting to give up hope, 'I doubt they've realized I'm gone. Let's be real, I want to be friends with Sasuke but he doesn't really care and Sakura is so busy obsessing over Sasuke that she doesn't see much else. Kakashi-sensei might notice, but who knows. I'm just a burden to them anyway.'

'Don't think those things, my jinchuriki is greater than that,' Kurama tried to smack sense into his human's mind.

'The adults only see you, and the kids find me annoying. I can't even do some of the simplest jutsus. I know I've come a long way, but they can go so much further without me. If I could release you from my body so you could escape I would. You may have done some bad things but you don't deserve to be power for a weapon.'

Kurama knew the boy meant what he said with his last sentence and simply said, 'Thank you.'

After a long silence which felt like hours to Naruto, the scientist came back, laughing wildly.

"You look like you've rested enough, no more coughing. Let's test something fun," he told the boy who remained quiet and unanswering.

"No response, eh?" the scientist hit a button, making the collar, which Naruto had already forgotten was on his neck, shock him until he fell forward, held back only by the shackles. After a few moments his vision and hearing started to come back, feeling in his body returning to normal.

"I just wanted to make sure that one was still working, and it looks like it is. However, we do have higher frequencies to test out," the madman turned the dial on the remote to the highest setting. As he pressed the button he watched as Naruto screamed, his body jolting in every direction, a burning smell wafting from where Naruto's wrists met the shackles. He let go of the button to see Naruto slump forward unconscious. The scientist walked into the cell and slapped Naruto awake, though Naruto was not entirely conscious.

"I need you awake for this next one," the scientist said harshly giving Naruto another slap before exiting the cell for his robot creation.

Naruto finally came to and was staring face to face with the robot.

"As I cannot do jutsus myself, I have created a robot that can. Well, I think it can, but you will be the first test subject," he informed Naruto who grunted in response.

The scientist punched in a code on the back of the robot and it started whirring to life. Naruto was suddenly transported to a forest, unshackled but still feeling the weakness from before. He attempted a jutsu but still nothing.

Naruto watched as his friends walked up.

"Hey Naruto," Sakura walked up.

"What's up loser?" Sasuke told him.

"You were late today," Kakashi said.

"Yeah, it's been a crazy day," Naruto was relieved to see familiar faces, "I'm not really sure what happened."

"You let your guard down and got caught," Sasuke told him.

Kakashi disappeared and Naruto felt his arms being bound.

"You let your guard down again," Kakashi whispered in his ear.

"You're so stupid sometimes," Sakura laughed.

The three continued to berate him for what felt like hours.

"You know you are in some sort of genjutsu right?" The fox asked.

"I know. I'm not sure if I could cancel it if I tried with the shackles, but they are right, aren't they?"

"What happened to the happy and always positive person you normally are?"

"It gets tiring after a while. You know what it's like being hated."

"Them hating me is understandable. But to hate you is just stemming from hatred of me. I'm sorry."

"I'm sorry too, you really aren't that bad."

"Naruto?" Kakashi gently shook his student.

'You need to wake up Naruto,' Kurama instructed.

Naruto opened his eyes and saw his teammates around him, "What happened?"

"You didn't show up for class so we came and looked for you," Sakura informed.

Naruto noticed his wrists were unshackled as Kakashi helped him stand.

"Where did that guy go? The scientist? And the two other guys?"

"We took care of them," Sasuke answered.

"Naruto, are you ok?" Kakashi asked.

Naruto shrugged as he slowly walked forward, his muscles protesting with every step.

"Naruto, I never realized how bad you had it," Sakura whispered.

"It's not that bad if it's all you know," Naruto responded leaving the cell. He followed a hallway and realized they were inside of a cave. He found the exit as he noticed anbu leaving with evidence. He was blinded by the sunlight but his eyes focused to realize they were on the outskirts of the village.

"Naruto, the Hokage will want to see you," Kakashi directed.

"Well, tell Granny I'll be there later. I'm going to go clean my apartment, I'm sure it's a mess."

"Sasuke and I can help you!"

"Sakura, you don't have to."

"You are our teammate, right? We should help each other out."

Naruto shrugged and let his teammates follow him back to the apartment. With three of them, it was quickly cleaned, probably cleaner than before the break-in.

Naruto was quickly back to his normal self with the help of his team and Kurama. Though they'd never admit it, Sakura and Sasuke started giving threatening looks to villagers who looked like they would bully Naruto. They knew they would have to deal with the fox eventually, but for now they focused on their training.


End file.
